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Single Cell Chromatin Accessibility of the Developmental bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994954; this version posted March 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Single cell chromatin accessibility of the developmental cephalochordate Dongsheng Chen1, Zhen Huang2,3, Xiangning Ding1,4, Zaoxu Xu1,4, Jixing Zhong1,4, Langchao Liang1,4, Luohao Xu5, Chaochao Cai1,4, Haoyu Wang1,4, Jiaying Qiu1,4, Jiacheng Zhu1,4, Xiaoling Wang1,4, Rong Xiang1,4, Weiying Wu1,4, Peiwen Ding1,4, Feiyue Wang1,4, Qikai Feng1,4, Si Zhou1, Yuting Yuan1, Wendi Wu1, Yanan Yan2,3, Yitao Zhou2,3, Duo Chen2,3, Guang Li6, Shida Zhu1, Fang Chen1,7, Qiujin Zhang2,3, Jihong Wu8,9,10,11 &Xun Xu1 1. BGI-shenzhen, Shenzhen 518083, China 2. Life Science College, Fujian Normal University 3. Key Laboratory of Special Marine Bio-resources Sustainable Utilization of Fujian Province, Fuzhou 350108, P. R. China 4. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China 5. Department of Neuroscience and Developmental Biology, University of Vienna 6. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China 7. MGI, BGI-Shenzhen, Shenzhen 518083, China 8. Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China 9. Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China 10. Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, China 11. State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China Abstract: The phylum chordata are composed of three groups: vertebrata, tunicate and cephalochordata. Single cell developmental atlas for typical species in vertebrata (mouse, zebrafish, western frog, worm) and tunicate (sea squirts) has been constructed recently. However, the single cell resolution atlas for lancelet, a living proxy of vertebrate ancestors, has not been achieved yet. Here, we profiled more than 57 thousand cells during the development of florida lancelet (Branchiostoma floridae), covering important processes including embryogenesis, organogenesis and metamorphosis. We identified stage and cluster specific regulatory elements. Additionally, we revealed the regulatory codes underlying functional specification and lineage commitment. Based on epigenetic features, we constructed the developmental bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994954; this version posted March 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. trajectory for lancelet, elucidating how cell fates were established progressively. Overall, our study provides, by far, the first single cell regulatory landscape of amphioxus, which could help us to understand the heterogeneity and complexity of lancet development at single cell resolution and throw light upon the great transition from simple chordate ancestor to modern vertebrates with amazing diversity and endless forms. Introduction: Vertebrate evolved through two rounds of ancient whole genome duplications, followed by functional divergence in terms of regulatory circuits and gene expression patterns1. Lancelets are derived from an ancient chordate lineage, and belong to the cephalochordate clade2. As the sister group of vertebrates and tunicates, cephalochordate showed great similarity to fossil chordates from Cambrian in terms of morphology and thus have been considered as “living fossils”3, or living proxies for the chordate ancestor. As a slow-evolving chordate species, amphioxus is a good model to explore evolution history and provide insights about vertebrate origin and evolution. Amphioxus has been considered as a key phylogenetic model animal about vertebrate origin 4. In contrast to tunicates, cephalochordates maintained their basic body plans since Cambrian, therefore study on cephalochordates could probably provide valuable insights about the patterning mechanisms conserved among chordates. Yang et al. performed RNAseq for Branchiostome, covering 13 development stages, ranging from fertilized egg to adults. In total, they identified 3423 genes changed significantly during the development, including the increase of translation associated genes and decrease of cell cycle genes5. Marletaz et al. performed whole genome sequencing for Branchiostome lanceolatum and constructed genomic profiles including transcriptome, histone modification, DNA methylation and chromatin accessibility at bulk level. This study revealed high conversation of cis elements and gene expression patterns between bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994954; this version posted March 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. vertebrates and amphioxus at earlier middle embryonic stage, supporting the hourglass model6. Although previous studies revealed key components and regulatory mechanisms of lancelet development, they fail to detect rare cell populations and rapid changing pathway signals during animal development because of the diversity of cell types and complicated cellular interactions. To understand the genomic and epigenomic landscapes of animal development, single cell sequencing methods have been widely employed in developmental biology. The developmental process for mouse, zebrafish, clawed frog, worm and ascidian have been investigated at single cell resolution7-11, which revealed cell lineages and developmental trajectories. These studies elucidate the dynamic gene expression profiles during the development of rodent, fish, nematode and proto-vertebrate. However, a cellular and molecular taxonomy of more ancient species such as amphioxus is still missing. In this study, we profiled the chromatin accessibility and gene expression of Branchiostoma floridae at bulk levels covering 18 continuous developmental stages, including sperm, oocyte, zygote, 2 cell, 8 cell, 16 cell, 64 cell, blastula, early gastrulation (early-gas or EG), late gastrulation (late-gas, or LG), early neurula (early-neu, or EN), middle neurula (mid-neu, or MN), late neurula (late-neu, or LN) , larva, early metamorphosis (early-meta, or EM), middle metamorphosis (mid-meta, or MM), late metamorphosis (late-meta, or LM). Meanwhile, we characterized the single cell chromatin accessibility from blastula to larva stage. Our study, for the first time, revealed the dynamic epigenetic of lancelet development at single cell revolution, which classified cells into different groups with distinct patterns of chromatin accessibility profiles. Moreover, we traced the turnover of cis regulatory elements of each cell lineage through the whole life cycle of Branchiostoma floridae. Results: Profiling of cis regulatory elements during amphioxus development bioRxiv preprint doi: https://doi.org/10.1101/2020.03.17.994954; this version posted March 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. To evaluate cis regulatory elements (CREs) dynamics of Branchiostoma floridae development, we performed assay for transposase-accessible chromatin with high throughput sequencing (ATACseq) for Branchiostoma floridae including 18 time points (Figure 1a). During the entire development period studied, we detected a total of 2,181,151 peaks after rigid filter criteria. To evaluate repeatability of each stage, we performed principal component analysis (PCA) (Figure S1a), which discriminated different development embryonic stages and indicated replicates of the same stage tended to share higher similarity. Genomic feature analysis (Figure S1b) showed more than 25% of peaks fell to the promoter regions. We found peaks located at promoter regions increased dramatically after early gastrulation stage and increased progressively from zygote to middle neurula stage, and decreased afterwards, which might indicate corresponding dynamics of regulatory elements during developmental stages. Interestingly neurula stage possesses the least number of peaks, but has the largest ratio of peaks within promoter regions. CREs of master regulators and signaling pathway components were under dynamic regulation during amphioxus development To pinpoint the profile of dynamic accessible regions during amphioxus development, we visualized ATACseq data of all time points using the integrative genomics viewer (IGV). Hox genes were reported to encode a family of transcriptional factors playing crucial roles in specifying body plans along the head-to-tail axis in various animals12. In Branchiostoma floridae, 15 Hox genes in total, existed in clusters on chromosome 17 within a 500kb range (Figure 1b). Based on our data,
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